changing command name classify.shared to classifyrf.shared

[mothur.git] / flowdata.cpp

diff --git a/flowdata.cpp b/flowdata.cpp
index f4605b6dbe1613fdb3e1a6beb1929a3585ff5fe7..7d61f8c265e060f2dc0002c94f69edfd054f89ae 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -68,9 +68,7 @@ string FlowData::getSequenceName(ifstream& flowFile) {
         flowFile >> name;
                
                if (name.length() != 0) { 
-            for (int i = 0; i < name.length(); i++) {
-                if (name[i] == ':') { name[i] = '_'; m->changedSeqNames = true; }
-            }
+            m->checkName(name);
         }else{ m->mothurOut("Error in reading your flowfile, at position " + toString(flowFile.tellg()) + ". Blank name."); m->mothurOutEndLine(); m->control_pressed = true;  }
         
                return name;
@@ -124,18 +122,40 @@ void FlowData::updateEndFlow(){
 }
 
 //**********************************************************************************************************************
-
+//TATGCT
+//1 0 0 0 0 1
+//then the second positive flow is for a T, but you saw a T between the last and previous flow adn it wasn't positive, so something is missing
+//Becomes TNT
 void FlowData::translateFlow(){
-       
        try{
-               sequence = "";
-               for(int i=0;i<endFlow;i++){
+        sequence = "";
+        set<char> charInMiddle;
+        int oldspot = -1;
+        bool updateOld = false;
+        
+        for(int i=0;i<endFlow;i++){
                        int intensity = (int)(flowData[i] + 0.5);
                        char base = baseFlow[i % baseFlow.length()];
+            
+            if (intensity == 0) { //are we in the middle
+                if (oldspot != -1) { charInMiddle.insert(base); }
+            }else if (intensity >= 1) {
+                if (oldspot == -1) { updateOld = true;  }
+                else {  //check for bases inbetween two 1's
+                    if (charInMiddle.count(base) != 0) { //we want to covert to an N
+                        sequence = sequence.substr(0, oldspot+1);
+                        sequence += 'N';
+                    }
+                    updateOld = true;
+                    charInMiddle.clear();
+                }
+            }
                        
                        for(int j=0;j<intensity;j++){
                                sequence += base;
                        }
+            
+            if (updateOld) { oldspot = sequence.length()-1;  updateOld = false; }
                }
         
                if(sequence.size() > 4){
@@ -144,7 +164,7 @@ void FlowData::translateFlow(){
                else{
                        sequence = "NNNN";
                }
-       }
+    }
        catch(exception& e) {
                m->errorOut(e, "FlowData", "translateFlow");
                exit(1);
@@ -170,6 +190,27 @@ void FlowData::capFlows(int mF){
 
 //**********************************************************************************************************************
 
+bool FlowData::hasGoodHomoP(){
+       
+       try{
+        
+        float maxIntensity = (float) maxHomoP + 0.49;
+
+        for(int i=0;i<endFlow;i++){
+            if(flowData[i] > maxIntensity){
+                return 0;
+            }
+        }
+               return 1;
+       }
+       catch(exception& e) {
+               m->errorOut(e, "FlowData", "hasMinFlows");
+               exit(1);
+       }
+}
+
+//**********************************************************************************************************************
+
 bool FlowData::hasMinFlows(int minFlows){
        
        try{